Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold12043.1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2435
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Found at i:1152 original size:37 final size:37
Alignment explanation
Indices: 1094--1164 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
1084 GCTCAGATGA
* *
1094 AATCTCCACATGAAGTTATCGGGTCTTACCCGGACAT
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAT
*
1131 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGA
1165 ATATATTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (37 bp):
AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAT
Found at i:1467 original size:37 final size:37
Alignment explanation
Indices: 1425--1495 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
1415 GCTCAGATGA
* *
1425 AATCTCCACATGAAGTTATCGGGTCTTACCCGGACAT
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAT
*
1462 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGA
1496 ATATATTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (37 bp):
AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAT
Found at i:1683 original size:331 final size:331
Alignment explanation
Indices: 1081--1741 Score: 1304
Period size: 331 Copynumber: 2.0 Consensus size: 331
1071 GGCAAGACCT
1081 TTAGCTCAGATGAAATCTCCACATGAAGTTATCGGGTCTTACCCGGACATAATCTCCACACGTAG
1 TTAGCTCAGATGAAATCTCCACATGAAGTTATCGGGTCTTACCCGGACATAATCTCCACACGTAG
1146 TCATCGGGTCTTACCCGGAATATATTTCCAAGTTTCATGTACATTTAATCACATGTTACAACATT
66 TCATCGGGTCTTACCCGGAATATATTTCCAAGTTTCATGTACATTTAATCACATGTTACAACATT
1211 CAAATCGACTGTCATATTTGTAATTCATTTGCCTCATCCAAAAATCTAATAATACACACCTTTCA
131 CAAATCGACTGTCATATTTGTAATTCATTTGCCTCATCCAAAAATCTAATAATACACACCTTTCA
1276 CCGTTTGTCATTTGGCCACAATATATATATACACATCTCGTACATATCTCACATTAGCCATTTGG
196 CCGTTTGTCATTTGGCCACAATATATATATACACATCTCGTACATATCTCACATTAGCCATTTGG
* *
1341 CTTTACCACATATCCATCTCATACACGTTTCGCATTAGCCATTCAGCCTTACCACATATATTCGT
261 CTTTACCACATATCCATCTCATACACGTTTCGCATTAGCCATTCAGCCTTACCACATATATACGG
1406 GTTCAG
326 GTTCAG
1412 TTAGCTCAGATGAAATCTCCACATGAAGTTATCGGGTCTTACCCGGACATAATCTCCACACGTAG
1 TTAGCTCAGATGAAATCTCCACATGAAGTTATCGGGTCTTACCCGGACATAATCTCCACACGTAG
1477 TCATCGGGTCTTACCCGGAATATATTTCCAAGTTTCATGTACATTTAATCACATGTTACAACATT
66 TCATCGGGTCTTACCCGGAATATATTTCCAAGTTTCATGTACATTTAATCACATGTTACAACATT
1542 CAAATCGACTGTCATATTTGTAATTCATTTGCCTCATCCAAAAATCTAATAATACACACCTTTCA
131 CAAATCGACTGTCATATTTGTAATTCATTTGCCTCATCCAAAAATCTAATAATACACACCTTTCA
1607 CCGTTTGTCATTTGGCCACAATATATATATACACATCTCGTACATATCTCACATTAGCCATTTGG
196 CCGTTTGTCATTTGGCCACAATATATATATACACATCTCGTACATATCTCACATTAGCCATTTGG
1672 CTTTACCACATATCCATCTCATACACGTTTCGCATTAGCCATTCAGCCTTACCACATATATACGG
261 CTTTACCACATATCCATCTCATACACGTTTCGCATTAGCCATTCAGCCTTACCACATATATACGG
1737 GTTCA
326 GTTCA
1742 CATTCATCAC
Statistics
Matches: 328, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
331 328 1.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (331 bp):
TTAGCTCAGATGAAATCTCCACATGAAGTTATCGGGTCTTACCCGGACATAATCTCCACACGTAG
TCATCGGGTCTTACCCGGAATATATTTCCAAGTTTCATGTACATTTAATCACATGTTACAACATT
CAAATCGACTGTCATATTTGTAATTCATTTGCCTCATCCAAAAATCTAATAATACACACCTTTCA
CCGTTTGTCATTTGGCCACAATATATATATACACATCTCGTACATATCTCACATTAGCCATTTGG
CTTTACCACATATCCATCTCATACACGTTTCGCATTAGCCATTCAGCCTTACCACATATATACGG
GTTCAG
Found at i:1768 original size:47 final size:49
Alignment explanation
Indices: 1704--1851 Score: 178
Period size: 47 Copynumber: 3.1 Consensus size: 49
1694 ACACGTTTCG
* *
1704 CATTAGCCATTCAGCCTTA-C-CACATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATATACGGGTTCACATTCATCA
* ** ** *
1751 CATTGGCCATTCGGCCTTATCTCACA-A-ACGCATGTTCACACTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATATACGGGTTCACATTCATCA
1798 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACAC--ATATATACGGGTTCACATTCATCA
1849 CAT
1 CAT
1852 GAAATCCTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 8
0.80 0.13 0.08
Matches are distributed among these distances:
47 56 0.68
48 2 0.02
49 5 0.06
50 1 0.01
51 18 0.22
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (49 bp):
CATTGGCCATTCGGCCTTATCACACATATATACGGGTTCACATTCATCA
Done.